Withholding consent on a nominee is the Senate's constitutional right, which is precisely what the Senate was doing when it refused to appoint Obama's nominees to the NLRB. Obama disregarded that right of the Senate to withhold their consent and made his appointments anyway, declaring on his own that the Senate was not in session when in fact the Senate was holding pro-forma session expressly for the purpose of withholding their consent to Obama's nominees.

I will note that the article above also points out that the Democrats' decision to nuke the filibuster made this case a bit less momentous in its outcome due to the fact that thanx to the Democrats, Presidents no longer have to try to obtain bipartisan support for their nominations. Democrats were all in favor of increasing the power of the presidency when their guy was in power--they are regretting it now, though. To his credit, at least Chuck Schumer advised against nuking the filibuster for presidential nominees. Now he has to live with this new power the Democrats gave the presidency, with no real ability to challenge Trumps nominations.

Perhaps you didn't read the whole article you posted.
"Obama made appointments to the National Labor Relations Board (NLRB) at a time when the Senate was holding pro forma sessions every three days precisely to thwart the president’s ability to exercise the power.

“The Senate is in session when it says it is,” Justice Stephen G. Breyer wrote for the court, stressing that if the Senate is able to conduct business, that is enough to keep the president from making recess appointments.

But the court stepped back from handing Obama — and those who will follow him in the Oval Office — a more substantial loss. A bare majority of the justices upheld, in theory at least, the president’s ability to make recess appointments when the Senate is indeed on extended break, saying history weighs in favor of a broad power.

I read the article just fine--It appears to me that you are just misinterpreting it. You seem to think that in our government, the President's prerogatives are absolute without any check against anything they want to do. Clearly your interpretation is incorrect, as ruled by the Supreme Court in a precedent setting 9-0 ruling against Obama.

The Supreme Court did rule that recess appointments are constitutionally sound--that does not mean that the court ruled in Obama's favor. All of Obama's nominations were ruled to have been appointed unconstitutionally in this case. He lost...full stop...because he overstepped his authority. The Senate was staying in session explicitly to deny Obama his choice so that he could not exercise what would be his right to appoint members as a recess appointment. Obama just decided on his own that he can just proclaim that the Senate is not in session and make his appointments. That was why he lost 9-0.